15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
- Source (raw)
- Browse (raw)
- How to Contribute
- Testers (1 / 74 / 0)
- KwaliteeBus factor: 2
- % Coverage
- License: perl_5
- Perl: v5.6.1
- Activity24 month
- Download (481.25KB)
- MetaCPAN Explorer
- Subscribe to distribution
- This version
- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Ewan Birney, Hilmar Lapp
- Methods overriden from BasePersistenceAdaptor
- Public methods specific to this module
- Private methods
Bio::DB::BioSQL::TermAdaptor - DESCRIPTION of Object
Give standard usage here
Term DB adaptor
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
Email firstname.lastname@example.org Email hlapp at gmx.net
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Function: Instantiates the persistence adaptor. Example : Returns : Args :
Title : get_persistent_slots Usage : Function: Get the slots of the object that map to attributes in its respective entity in the datastore. Slots should be methods callable without an argument. Example : Returns : an array of method names constituting the serializable slots Args : the object about to be inserted or updated
Title : get_persistent_slot_values Usage : Function: Obtain the values for the slots returned by get_persistent_slots(), in exactly that order. The reason this method is here is that sometimes the actual slot values need to be post-processed to yield the value that gets actually stored in the database. E.g., slots holding arrays will need some kind of join function applied. Another example is if the method call needs additional arguments. Supposedly the adaptor for a specific interface knows exactly what to do here. Since there is also populate_from_row() the adaptor has full control over mapping values to a version that is actually stored. Example : Returns : A reference to an array of values for the persistent slots of this object. Individual values may be undef. Args : The object about to be serialized. A reference to an array of foreign key objects if not retrievable from the object itself.
Title : get_foreign_key_objects Usage : Function: Gets the objects referenced by this object, and which therefore need to be referenced as foreign keys in the datastore. Note that the objects are expected to implement Bio::DB::PersistentObjectI. An implementation may obtain the values either through the object to be serialized, or through the additional arguments. An implementation should also make sure that the order of foreign key objects returned is always the same. Note also that in order to indicate a NULL value for a nullable foreign key, either put an object returning undef from primary_key(), or put the name of the class instead. DO NOT SIMPLY LEAVE IT OUT. Example : Returns : an array of Bio::DB::PersistentObjectI implementing objects Args : The object about to be inserted or updated, or undef if the call is for a SELECT query. In the latter case return class or interface names that are mapped to the foreign key tables. Optionally, additional named parameters. A common parameter will be -fkobjs, with a reference to an array of foreign key objects that are not retrievable from the persistent object itself.
Title : attach_foreign_key_objects Usage : Function: Attaches foreign key objects to the given object as far as necessary. This method is called after find_by_XXX() queries, not for INSERTs or UPDATEs. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object to which to attach foreign key objects. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
Title : store_children Usage : Function: Inserts or updates the child entities of the given object in the datastore. The implementation can assume that all of the child objects are already Bio::DB::PersistentObjectI. Ontology terms have synonyms and dbxrefs as children. Example : Returns : TRUE on success, and FALSE otherwise Args : The Bio::DB::PersistentObjectI implementing object for which the child objects shall be made persistent. A reference to an array of foreign key values, in the order of foreign keys returned by get_foreign_key_objects().
Title : attach_children Usage : Function: Possibly retrieve and attach child objects of the given object. This is needed when whole object trees are supposed to be built when a base object is queried for and returned. An example would be Bio::SeqI objects and all the annotation objects that hang off of it. This is called by the find_by_XXXX() methods once the base object has been built. An ontology term has synonyms and dbxrefs as children. Example : Returns : TRUE on success, and FALSE otherwise. Args : The object for which to find and to which to attach the child objects.
Title : remove_children Usage : Function: This method is to cascade deletes in maintained objects. Example : Returns : TRUE on success and FALSE otherwise Args : The persistent object that was just removed from the database. Additional (named) parameter, as passed to remove().
Title : instantiate_from_row Usage : Function: Instantiates the class this object is an adaptor for, and populates it with values from columns of the row. This implementation calls populate_from_row() to do the real job. Example : Returns : An object, or undef, if the row contains no values Args : A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots(). Optionally, the object factory to be used for instantiating the proper class. The adaptor must be able to instantiate a default class if this value is undef.
Title : populate_from_row Usage : Function: Instantiates the class this object is an adaptor for, and populates it with values from columns of the row. Example : Returns : An object, or undef, if the row contains no values Args : The object to be populated. A reference to an array of column values. The first column is the primary key, the other columns are expected to be in the order returned by get_persistent_slots().
Title : get_unique_key_query Usage : Function: Obtain the suitable unique key slots and values as determined by the attribute values of the given object and the additional foreign key objects, in case foreign keys participate in a UK. Example : Returns : One or more references to hash(es) where each hash represents one unique key, and the keys of each hash represent the names of the object's slots that are part of the particular unique key and their values are the values of those slots as suitable for the key. Args : The object with those attributes set that constitute the chosen unique key (note that the class of the object will be suitable for the adaptor). A reference to an array of foreign key objects if not retrievable from the object itself.
Title : remove_synonyms Usage : Function: Removes synonyms for the given ontology term. Example : Returns : TRUE on success, and FALSE otherwise. Args : The persistent term object for which to remove the synonyms (a Bio::DB::PersistentObjectI compliant object with defined primary key).
Title : store_synonym Usage : Function: Stores a synonym for an ontology term. Example : Returns : TRUE on success, and FALSE otherwise. Args : The persistent term object for which to store the synonym (a Bio::DB::PersistentObjectI compliant object with defined primary key). The synonym to store (a scalar).
Title : get_synonyms Usage : Function: Retrieves the synonyms for an ontology term and adds them the term's synonyms. Example : Returns : TRUE on success, and FALSE otherwise. Args : The persistent term object for which to retrieve the synonyms (a Bio::DB::PersistentObjectI compliant object with defined primary key).
These are mostly convenience and/or shorthand methods.
Title : _ont_adaptor Usage : $obj->_ont_adaptor($newval) Function: Get/set the ontology persistence adaptor. Example : Returns : value of _ont_adaptor (a Bio::DB::PersistenceAdaptorI object) Args : on set, new value (a Bio::DB::PersistenceAdaptorI object or undef, optional)
Title : _build_dblink Usage : Function: Create a Bio::Annotation::DBLink object for a flat dbxref string. Example : Returns : A Bio::Annotation::DBLink instance Args : The dbxref as a flat string (DB:acc.version format)
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.